Using genomic fingerprinting by arbitrarily primed PCR (AP-PCR), we have shown that the species Borrelia burgdorferi is actually comprised of at least three distinct phyletic groups, whose level of divergence approaches that of distinct species by several criteria (Welsh et al., 1992). The validity of AP-PCR as a phylogenetic tool has been corroborated by multilocus enzyme electrophoresis (MEE) and other methods, as we will demonstrate. Here, we propose to apply genomic fingerprinting and other methods to resolve several questions in the population genetics of B. burgdorferi. First, we will compare phylogenetic analysis using AP-PCR with MEE for the ECOR collection. We will refine the correlation between genetic distances measured by MEE and AP-PCR using this data. Second, we will continue to explore the number and distribution of distinct phyletic groups of B. burgdorferi, expecting to reveal distinct species or subspecies, and generally outline the genetic structure of the population. In this part of the study, we will determine whether the intraspecies phylogeny of the spirochete correlates with regional geographics within North America, as has been demonstrated for B. burgdorferi in Eurasia. We will also compare Group I B. burgdorferi from both continents, to determine the genetic relationship between the two populations. Third, we will determine if B. burgdorferi from different phyletic groups have different preferred hosts, including human. Fourth, we will seek evidence of naturally occurring genetic recombination between strains of B. burgdorferi by comparing DNA sequence information and constructing gene trees. Fifth, we will seek evidence for the horizontal movement of plasmids between different branches of the phylogenetic tree, using AP-PCR homoplasy, comparisons of plasmid profiles and Southern blotting.